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NAME
        bbregister

SYNOPSIS
        bbregister --s <subj> --mov <volid> --reg <regfile> \
                --<contrast>

DESCRIPTION
        This program performs within-subject, cross-modal registration using a
        boundary-based cost function. The registration is constrained to be 6
        DOF (rigid). It is required that you have an anatomical scan of the
        subject that has been analyzed in freesurfer.

POSITIONAL ARGUMENTS
        None

REQUIRED FLAGGED ARGUMENTS
bbregister is a program to perform within-subject, cross-modal registration using a
boundary-based cost function. The registration is constrained to be 6
DOF (rigid). It is required that you have an anatomical scan of the
subject that has been analyzed in freesurfer. Those using bbregister should site: Greve, D. N., and Fischl, B. (2009). "Accurate and robust brain image alignment using boundary-basedregistration." Neuroimage, 48, 63-72. <<BR>>

REQUIRED FLAGGED ARGUMENTS <<BR>>
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OPTIONAL FLAGGED ARGUMENTS OPTIONAL FLAGGED ARGUMENTS <<BR>>

bbregister is a program to perform within-subject, cross-modal registration using a boundary-based cost function. The registration is constrained to be 6 DOF (rigid). It is required that you have an anatomical scan of the subject that has been analyzed in freesurfer. Those using bbregister should site: Greve, D. N., and Fischl, B. (2009). "Accurate and robust brain image alignment using boundary-basedregistration." Neuroimage, 48, 63-72.

REQUIRED FLAGGED ARGUMENTS

  • --s subject
    • FreeSurfer subject name as found in $SUBJECTS_DIR.

    --mov volid
    • "Moveable" volume. This is the template for the cross-modal volume. Eg, for fMRI, it is the volume used for motion correction.
    --reg register.{dat,lta}
    • Output FreeSurfer registration file (tkregister-style or LTA format).

    --vsm VoxelShiftMap

    • Include B0 distortion correction while performing registration. A voxel shift map can be created from a B0 map

      with the epidewarp.fsl script (in FreeSurfer)

    Initialization Arguments
    --init-coreg (Default)

    --no-coreg-ref-mask
    • Do NOT use aparc+aseg.mgz as a reference mask. It will not attempt to use aparc+aseg if it is not there.
    --init-header
    • Assume that the geometry information in the cross-modal and anatomical are sufficient to get a close voxel-to-voxel registration. This usually is only the case if they were acquired in the same session.
    --init-reg initregfile
    • Supply an initial registration matrix; can be LTA.
    Contrast Arguments (one required) --t1
    • Assume t1 contrast, ie, White Matter brighter than Grey Matter
    --t2
    • Assume t2 contrast, ie, Gray Matter brighter than White Matter
    --bold
    • Same as --t2
    --dti
    • Same as --t2

OPTIONAL FLAGGED ARGUMENTS

  • --int intvol
    • Supply a volume to use an an intermediate volume when performing registration. This is useful for when the cross-modal is volume is a partial field-of-view (FoV). If you acquire in the same session a whole-head FoV, then pass the whole-head as the intermediate and the partial as the moveable.
    --mid-frame
    • reg to middle frame (not with --frame)
    --frame frameno
    • reg to frameno (default 0=1st)
    --template-out template
    • save template (good with --frame)
    --o outvol
    • resample mov and save as outvol
    --s-from-reg reg
    • get subject name from regfile
    --rms rmsfile
    • RMS change in cortical surface position
    --fslmat flirt.mtx
    • output an FSL FLIRT matrix
    --lta output.lta
    • output an LTA registration matrix (This flag can be used along with or instead of --reg!)
    --lh-only
    • only use left hemi
    --rh-only
    • only use right hemi
    --slope1 slope1
    • cost slope for 1st stage (default is 0.5)
    --slope2 slope2
    • cost slope for 2nd stage (default is 0.5)
    --offset2 offset2
    • cost offset for 2nd stage (default is 0)
    --tol1d tol1d
    • 2nd stage 1D tolerance
    --tol tol
    • 2nd stage loop tolerance (same as --tolf)
    --tolf tolf
    • 2nd stage loop tolerance (same as --tol)
    Be careful making these more stringent as they can cause underflows

    and NaNs.
    --nmax nPowellMax

    • set max number of iterations (default 36)
    --rand-init randmax
    • randomly change input to 1st stage reg
    --gm-proj-frac frac
    • default is 0.5
    --gm-proj-abs abs
    • use absolute instead of relative
    --wm-proj-abs dist
    • 2nd stage, default is 2mm
    --proj-abs dist
    • use wm and gm proj abs in 2nd stage
    --subsamp nsub
    • 2nd stage vertex subsampling, default is 1
    --nearest
    • 2nd stage, use nearest neighbor interp (defalt is trilinear)
    --epi-mask
    • mask out brain edge and B0 regions (1st and 2nd stages)
    --no-cortex-label
    • Do not use ?h.cortex.label to mask.
    --label labelfile
    • Use label to mask. Only vertices in the label are used.
    --brute1max max
    • pass 1 search -max to +max (default 4)
    --brute1delta delta
    • pass 1 search -max to +max step delta (default 4)
    --subsamp1 nsubsamp
    • pass 1 vertex subsampling (default 1)
    --no-pass1
    • turn off pass 1
    --no-brute2
    • turn off brute force search on pass 2
    --surf surfname
    • change surface to surfname from ?h.white
    --surf-cost basename
    • saves final cost as basename.?h.mgh
    --surf-con basename
    • saves final contrast as basename.?h.mgh
    --init-surf-cost basename
    • saves initial cost as basename.?h.mgh
    --init-reg-out outinitreg
    • save initial reg
    --initcost initcostfile
    • save initial cost
    --cost-fail costvalue
    • exit with error if the final cost exceeds costvalue
    --12, --9, --6
    • Use 12 or 9 or 6 DOF (6 is default)
    --coreg-dof coregDOF
    • Set dof to use for mri_coreg
    --spm-nii
    • Use NIFTI format as input to SPM when using --init-spm (spmregister). Ordinarily, it uses ANALYZE images to be compatible with older versions of SPM, but this has caused some left-right reversals in SPM8.
    --feat featdir
    • FSL FEAT directory. Sets mov to featdir/example_func, uses --init-fsl, --bold, sets reg to featdir/reg/freesurfer/ anat2exf.register.dat. This replaces reg-feat2anat.
    --fsl-bet-mov
    • When using FSL, apply BET to mov volume (turned by default).
    --init-rr
    • Initialize using NMI as implemented in mri_robust_register.
    --init-fsl
    • Initialize using FSL FLIRT (requires that FSL be installed).
    --init-spm
    • Initialize using SPM spm_coreg (requires that SPM and matlab be installed).
    --tmp tmpdir
    • temporary dir (implies --nocleanup)
    --nocleanup
    • do not delete temporary files
    --version
    • print version and exit
    --help
    • print help and exit

EXAMPLE 1

  • Intialize with FLIRT, view result with tkregister2: bbregister --s bert --mov func.nii --init-fsl --reg register.dat tkregister2 --mov func.nii --reg register.dat --surf

EXAMPLE 2

  • Intialize with SPM, view result with tkregister2: bbregister --s bert --mov func.nii --init-spm --reg register.dat tkregister2 --mov func.nii --reg register.dat --surf

EXAMPLE 3

  • Register a partial FoV using whole FoV as intermdediate: bbregister --s bert --mov partial.nii --init-fsl --int whole.nii --reg register.partial.dat tkregister2 --mov partial.nii --reg register.partial.dat --surf

REPORTING

bbregister (last edited 2019-07-11 13:35:54 by DougGreve)